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16 protocols using ultra turrax t8 homogenizer

1

Organ Extraction and RNA Isolation

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At predetermined time points after the disease onset mice were anesthetized with a ketamine/xylazine (Biowet, Poland) cocktail (100 mg/kg of ketamine and 10 mg/kg of xylazine) and perfused through the left cardiac ventricle with ice cold phosphate-buffered saline (PBS; Sigma-Aldrich, Poland) with heparin. The organs selected for further analysis were dissected and homogenized in RLT buffer (Qiagen, Poland) or Trizol reagent (Invitrogen, Poland) using Ultra Turrax T8 homogenizer (Ika-Werke, Germany). Total cellular RNA from brains was isolated with RNeasy kits (Qiagen, Poland) according to the manufacturer’s instructions. The concentration and purity of RNA were determined by spectroscopy at 260/280 nm.
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2

Protein Extraction from Brain Tissue

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The brain tissues (∼0.4 g) were thawed on ice and homogenized using Ultra-turrax T8 homogenizer (IKA-Werke GmbH & Co. KG, Germany) in 500 µl solubilization buffer containing 8M urea, 2% (w/v) CHAPS, 0.2% sodium orthovanadate and 1× concentration of protease inhibitor cocktail for mammalian cells and tissue extracts (Sigma Aldrich, USA). The supernatant was collected by centrifugation and subjected to three pulses of sonication on ice followed by centrifugation at 20,000× g for 30 min at 4°C for the recovery of total soluble proteins. Protein extraction from Neuro2a cells was carried out in a similar manner. Protein concentration was quantified in supernatants by Bradford Protein Assay kit (Bio-Rad, USA) as per manufacturer's instructions and the extraction procedure was carried out according to [13] (link).
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3

Total RNA Isolation from Mouse Tissues

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Total RNA was isolated from a pool of 20 OCs, SGs, SVs and from 20–40 mg brain of 5-day-old C57/BL6 mice pups using the RNAeasy Minikit (Qiagen, Hombrechtikon, Switzerland) including DNase treatment according to the supplier’s instructions. To homogenize the tissues, we used the Ultra-Turrax T8 homogenizer (IKA-Werke, Staufen, Germany). The quantity and quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA). The 260/280 nm ratio of all our samples was between 1.8 and 2.1.
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4

Optimizing Metabolite Extraction from Tissues

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Each flash frozen tissue was homogenized using an ULTRA-TURRAX T8 homogenizer (IKA®-WERKE GmbH & Co., Germany) in 400 µl methanol (MeOH), vortexed for 60 s before being centrifuged using a Force 7 Fisher Scientific UK Limited (Leicestershire, UK) at 13,000 rpm/g for 5 min. The supernatant was collected using a micropipette syringe and formed the polar tissue extracts. The residue was extracted with 400 µl dichloromethane (DCM), vortexed for 60 s and centrifuged at 13,000 rpm/g for 10 mins. The supernatant was also collected and formed the non-polar tissue extracts. Wet homogenization combined with direct extraction has been described as one of the best methods for metabolite extraction from tissues as it gives one of the best metabolite reproducibility and improves the extraction process [20]. The whole procedure was performed in the cold with the aid of dry ice. The time periods employed were predetermined from preliminary experiments. The supernatant was collected using a micropipette syringe and dried in pre-weighed vials in preparation for further NMR and MS measurements.
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5

Metabolic Stability of Radioligand Peptides

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All animal experiments were approved by the Austrian Ministry of Science (BMWF-66.011/0075- WF/V/3b/2016) and performed in accordance with the Austrian Animal Protection Act. Metabolic studies characterizing the stability of selected radioligands against enzymatic degradation were carried out in 7 to 8 week old female BALB/c mice (Charles River, Sulzfeld, Germany). The mice (two animals for each peptide) were intravenously injected into a lateral tail vein with 5–10 MBq of the 111In-labeled peptide derivatives, corresponding to 2 nmol total peptide. At the time point of 10 min p.i. the animals were euthanatized by cervical dislocation. A sample of urine and blood was immediately collected. Liver and kidneys were dissected, mixed with 20 mM HEPES buffer pH 7.3 (1:1, w/v) and homogenized using an Ultra-Turrax T8 homogenizer (IKA-Werke, Staufen, Germany) for 1 min. All samples taken were analyzed by analytical HPLC using the low-sensitivity loop for urine and the high-sensitivity loop for blood, liver and kidney. Before injection into the HPLC system, all samples except urine were treated with ACN and diluted with water as described for stability studies in human serum. The percentage of intact radiopeptide in the analyzed samples was calculated by integration of the different peaks found in the radiochromatogram using Chromeleon Dionex Software (Version 7.2.9.11323).
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6

Cytokine Quantification in Porcine Tissues

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Pieces weighing between 80 and 320 mg were homogenized in lysis buffer (15 mM Tris, pH 7.4, 150 mM NaCl, 1 mM CaCl2, 1 mM MgCl2, 0.5 % Triton X-100), with addition of protease inhibitor (Thermo Scientific, Waltham, MA, USA) using an IKA Ultra-Turrax T8 homogenizer (IKA-Werke, Staufen im Breisgau, Germany). Homogenates were centrifuged at 300×g at 4 °C for 10 minutes. Supernatants were kept at −80 °C until assay. Cytokine content was assessed using a DuoSet enzyme-linked immunosorbent assay (ELISA) system (R&D Systems, Minneapolis, MN, USA), for porcine tumor necrosis factor (TNF)-α, interleukin (IL)-1β/IL-1F2, and IL-6 according to the manufacturer’s instructions. The detection limits of the assays were 125 pg/ml for TNF-α, 62.5 pg/ml for IL-1β/IL-1F2, and 125 pg/ml for IL-6. Total protein content of the supernatant was measured using a Coomassie Plus Assay (Thermo Scientific) according to the manufacturer’s instructions. Cytokine content of tissue lysates were normalized against total protein content of the homogenate.
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7

Brain Tissue Protein Extraction

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The brain tissues were thawed on ice and homogenized using Ultra-turrax T8 homogenizer (IKA-Werke GmbH & Co. KG, Germany) in solubilization buffer containing 8M urea, 2% (w/v) CHAPS (3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate), 0.2% sodium orthovanadate and 1 × concentration of protease inhibitor cocktail (Sigma Aldrich, St. Louis, MO, USA). The supernatant was collected by centrifugation and subjected to three pulses of sonication on ice followed by centrifugation at 20,000 × g for 30 min at 4 °C for the recovery of total soluble proteins. Protein extraction from Neuro2a cells was carried out in a similar manner. The rest of the extraction procedure was done according to ref. 51 (link).
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8

MMP-9 Inhibitor Treatment on Rat Pup SGNs

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6 SGNs of 5-day-old WS rat pups for each experimental condition were cultured and treated with 500 nM MMP-9 inhibitor (Calbiochem) as described above for 3 h and placed separately in RNAlater (Qiagen, Hombrechtikon, Switzerland). RNA isolation was performed using the RNAeasy Minikit (Qiagen, Switzerland) including DNase treatment according to the supplier’s instructions. An Ultra-Turrax T8 homogenizer (IKA- Werke, Staufen, Germany) was used to homogenize the tissues. The quantity and quality of the isolated RNA were determined with NanoDrop ND 1000 (NanoDrop Technologies, DE, USA). The 260/280 nm ratio of all our samples was between 1.8 and 2.1.
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9

In Vivo Stability of Radiolabeled Peptides

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Metabolic and biodistribution studies were performed in accordance with the ethical standards of the institution and approved by the Austrian Ministry of Science (BMWFW-66.011/0072-V/3b/2019).
In vivo stability studies of [177Lu]Lu-1 and [177Lu]Lu-2 were carried out in 5–7-week-old female BALB/c mice (Charles River Laboratories, Sulzfeld, Germany; n = 6). A higher radioactivity of ~37 MBq in a total volume of ~150 µL in PBS/0.5% BSA, corresponding to ~1 nmol total peptide, was administered into the mice intravenously through a lateral tail vein to increase the detectability of potential radiometabolites by radio-HPLC. The mice were euthanized by cervical dislocation after 10 (n = 2) and 30 (n = 1) min post injection and the urine and a venous blood sample were collected at the time of sacrifice. Liver and kidneys were dissected and homogenized in 20 mM HEPES buffer pH 7.3 (1:1, v/v) with an Ultra-Turrax T8 homogenizer (IKA-Werke, Staufen, Germany) for 1 min at RT. Prior to the radio-HPLC analysis, the samples of blood, kidney, and liver homogenates were treated with ACN to precipitate proteins (1:1, v/v), centrifuged (2000× g, 2 min) and the supernatant was diluted with water (1:1, v/v). Urine was diluted 1:4 with water before injection.
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10

Skeletal Muscle Protein Extraction

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We used skeletal muscle which were isolated for previously published study (See extended methods Schönke et al.). Frozen gastrocnemius muscles were crushed using mortar and pestle. Powdered muscle was homogenized using Ultra Turrax T8 homogenizer (IKA Labortechnik, Staufen im Breisgau, Germany) in 4% SDS buffer (100 mm Tris-HCl, pH 7.4). Protein lysates were boiled at 100 °C for 5 mins. Lysates were sonicated using a tip and centrifuged at 16,000 × g for 10 mins followed by reduction and alkylation as described above, the supernatant was then processed using FASP or PAC or frozen until further analysis.
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